It is the network of developmental interactions, rather than the gene, that is the focus of selection.


Well THE hot new topic around will be Epigentics. So lots of what is being arguing 'round here may be only part of the story.
Back when Thomas Kuhn published on science thinking, someone came along with the notion of the "anomaly box". When trying to form basic theory, anomalies are stored away. Later when things are more settled, the box is dusted off and exceptions are examined. It may be Genetics time to look at its anomaly box


Quote:


The late 20th century version of the Modern Synthesis assumed:

1. Heredity occurs through the transmission of germ-line genes. Genes are discrete units of DNA that are located in chromosomes. Hereditary variations are the result of differences in DNA base sequence. There are no inherited variations that cannot be expressed in terms of inherited genetic differences.
2. Hereditary variation is the consequence of (i) the many random combinations of pre-existing alleles that are generated by the sexual processes; and (ii) new variations (mutations) resulting from accidental changes in DNA. Hereditary variation is not affected by the developmental history of the individual. There is no “soft inheritance.”
3. Heritable variations usually have small effects, and evolution is typically gradual. Through the selection of individuals with phenotypes that make them slightly more adapted to their environment than are other individuals in the population, some alleles increase in frequency. Mutation pressure is not an important factor in evolution. With a few exceptions, macroevolution is continuous with microevolution, and does not require any additional processes.
4. The ultimate unit of selection is the gene. Although genes interact and the interactions are often non-linear, the additive fitness-effects of single genes (which can be extracted from the fitness effects of the developmental networks in which they participate) drive evolution by natural selection. The genetic-developmental network and the phenotype it generates is not heritable and cannot be a unit of evolution.
5. Morphological innovations, like all innovations, are the results of gene mutations that, when beneficial, accumulate over time and lead to a qualitatively new form. Generic, physical-chemical properties of biological matter, which underlie plasticity, have no role in morphological and physiological innovations other than specifying the boundaries of the forms that are possible.
6. The targets of selection are individuals, which are well-defined entities. Although conspecifics in groups interact and may co-evolve with each other as well as with their symbionts and parasites, group selection and community selection are rare. Species selection may exist but is of marginal significance. The community is only rarely a target of selection, and species selection cannot explain the main patterns of macroevolution.
7. Evolution occurs through modifications from a common ancestor, and is based on vertical descent. Horizontal transfer of genes or other types of information has only minor significance, and does not alter the basic branching structure of phylogenies. The main pattern of evolutionary divergence is, at all times and for all taxa, tree-like, not web-like.

Biologists are now questioning each of these assumptions, arguing that:
1. Heredity involves more than DNA. There are heritable variations that are independent of variations in DNA sequence, and they have a degree of autonomy from DNA variations. These non-DNA variations can form an additional substrate for evolutionary change, and also guide genetic evolution (Jablonka and Lamb, 1995, 2005; Jablonka and Raz, in press).
2. Soft inheritance, the inheritance of developmentally induced and regulated variations, exists and is likely to be important. It involves both non-DNA variations and developmentally-induced variations in DNA sequences (Jablonka and Lamb, 2005, 2008).
3. The rate at which heritable variations appear is sometimes higher in stressful conditions, and the spectrum of variations may be different, involving amplification, transposition, and massive, heritable, gene-activation and inactivation (see for example Levy and Feldman, 2004; Cullis, 2005). Such changes can lead to saltational evolution (Jablonka and Lamb, 2008; Lamm and Jablonka, 2008). Furthermore, variations in the expression and organization of a small set of genes that seems to be common to the development in all animal phyla can have dramatic phenotypic effects (Carroll, 2005). Macroevolution may be a consequence of changes in these core genes as well as the operation of stress-induced mechanisms that result in systemic mutations and genome re-patterning.
4. It is the network of developmental interactions, rather than the gene, that is the focus of selection. A gene’s expression and the scope of its effects depend not only on its own intrinsic nature, but also – and often much more – on the regulatory structure of the developmental network in which it is integrated (Wilkins, 2002; West-Eberhard, 2003; Wray, Purugganam and Gavrilets, chapter ??). Developmental networks are commonly modular, and are usually stable during phenotypic evolution.
5. Generic and evolved mechanisms that generate phenotypic plasticity have played a major role in evolution, initiating morphological and behavioral transformations (Forgács and Newman, 2005; Kirschner and Gerhard, 2005; Newman and Müller, 2006; Newman, chapter?; Müller, chapter ?; Kirschner, chapter ?; Pigliucci, chapter ?).
6. Group selection, involving selection of interactions among cooperating group members, is common (Sober and Wilson, 1998; Wilson, chapter ?). Since many organisms (including humans) contain symbionts and parasites that are transferred from one generation of the “host” to the next, it may be necessary to consider such communities as targets of selection (Zilber-Rosenberg and Rosenberg, 2008). Many patterns of macroevolutionary change are the outcome of selection at the species level and above (Jablonski, 2005, chapter ?).
7. The “Tree Of Life” pattern of divergence, which was supposed to be universal, fails to explain all the sources of similarities and differences between taxa. Sharing whole genomes (through hybridization, symbiosis and parasitism) and partial exchange of genomes (through various types of horizontal gene transfer) lead to web-like patterns of relations (Arnold, 2006; Goldenfeld and Woese, 2007). These web-like patterns are particularly evident in some taxa (e.g. plants, bacteria), and in special circumstances (e.g. during the initial stages that follow genome sharing or transfer). Co-evolution between viruses, and between viruses and their cellularized hosts, is an ongoing feature of evolution (Villarreal, 2005).
In this chapter we are focusing mainly on the first two of these challenges and some aspects of the third, but epigenetic inheritance undoubtedly also has significant implications for all of the other challenges to the Modern Synthesis that we have listed.

The epigenetic turn
Epigenetic-oriented approaches to evolution all have the developing phenotype rather than the gene as their starting point, and focus on aspects of development that lead to flexibility and adjustment when the environment or the genome changes. Although their roots are old, these approaches became influential during the 1990s, and today are an important part of the alternative view of evolution that is taking shape. We call this revival, extension and elaboration of epigenetic approaches to evolution the “epigenetic turn.”


http://www.mfo.ac.uk/files/images/Jablonka-ms_MPGM_EEEMclean.doc

now expanded into
Jablonka et al. Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution. The Quarterly Review of Biology, 2009; 84 (2): 131 DOI: 10.1086/598822